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Estimated time of infection vs. confirmed infections

Following the ideas from Tomas Pueyo's Medium post "Coronavirus: Why You Must Act Now" [1], we assume the average time from infection to death at 23 days [2]. The data is pulled from the COVID-19 Data Repository by Johns Hopkins CSSE [3] every hour. Countries with a minimnum of 1000 confirmed cases and 40 confirmed deaths are included in this analysis.

The time from infection to death is equal to the incubation period plus the time from symptoms to death. This is used to estimate the time of the infections that lead to the observed deaths. We take the last fatality rate per country (total_cases/total_deaths) to estimate the number of infections that are responsible for the observed deaths.

In the figures below, you can observe successive waves of infections (dashed), detections (black) and deaths (red) for each country. The upper panel shows the absolute number of events. The dashed lines show the estimated number of infections. The lower panel shows the normalized number of events. Here the temporal delay between the waves and the relative change between each other can be observed.

[1] https://medium.com/@tomaspueyo/coronavirus-act-today-or-people-will-die-f4d3d9cd99ca

[2] https://github.com/midas-network/COVID-19/tree/master/parameter_estimates/2019_novel_coronavirus

[3] https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series

US
Brazil
India
Mexico
Russia
Peru
United Kingdom
Indonesia
Italy
Iran
Colombia
France
Argentina
Germany
Ukraine
South Africa
Spain
Poland
Turkey
Romania
Philippines
Chile
Hungary
Czechia
Ecuador
Malaysia
Canada
Bulgaria
Pakistan
Bangladesh
Belgium
Vietnam
Tunisia
Iraq
Thailand
Egypt
Netherlands
Bolivia
Burma
Greece
Portugal
Japan
Kazakhstan
Paraguay
Guatemala
Sweden
Slovakia
Morocco
Sri Lanka
Austria
Bosnia and Herzegovina
Georgia
Serbia
Jordan
Switzerland
Nepal
Croatia
Honduras
Moldova
Saudi Arabia
Lebanon
Cuba
Israel
Azerbaijan
Armenia
North Macedonia
Panama
Costa Rica
Afghanistan
Lithuania
Ethiopia
Uruguay
Algeria
Ireland
Libya
Slovenia
Kenya
Belarus
Venezuela
West Bank and Gaza
Zimbabwe
China
Latvia
Dominican Republic
South Korea
Oman
El Salvador
Zambia
Namibia
Uganda
Sudan
Albania
Denmark
Kosovo
Nigeria
Cambodia
Syria
Kyrgyzstan
Kuwait
Botswana
Jamaica
Montenegro
Trinidad and Tobago
Malawi
United Arab Emirates
Australia
Mongolia
Yemen
Mozambique
Senegal
Estonia
Cameroon
Angola
Uzbekistan
Finland
Bahrain
Rwanda
Somalia
Eswatini
Ghana
Suriname
Norway
Congo (Kinshasa)
Guyana
Madagascar
Luxembourg
Taiwan*
Mauritania
Singapore
Haiti
Tanzania
Cote d'Ivoire
Bahamas
Fiji
Lesotho
Mali
Qatar
Cyprus
Belize
Papua New Guinea
Malta
Guinea
Congo (Brazzaville)
Cabo Verde
Burkina Faso
Saint Lucia
Gabon
Maldives
Barbados
Togo
Mauritius
Laos
Nicaragua
Hong Kong
Djibouti
Equatorial Guinea
Benin
South Sudan
Andorra
Seychelles
Tajikistan
Timor-Leste
Central African Republic

Ahead of the curve

Some countries start testing the population earlier in the outbreak than others. The time delay between the wave of deaths and the wave of confirmed cases is indicative for how early a country is detecting new cases ahead of the increase of deaths. Earlier detection means a better chances for successful isolation of an infected person and treatment of the desease.

We measure the distance of the maximum of cumulative deaths and new deaths to the number of infections to estimate the progression of the infection across countries.

If, in the early phase of the infection wave, the number of deaths rises faster than the number of confirmed cases, the distance drops, indicating that

A comparison of countries with respect to their mean time for reponse is presented below.

To determine the above values, we plot the number of confirmed cases (solid black lines) and the number of deaths (dashed black lines). From this, we measure the distance of the day of maximum deaths (dashed red lines) to the day of confirmed cases at this y-value.

The distance is indicative for how fast the humber of confirmed cases increases comapred to the increase of the number of deaths.

US
Brazil
India
Mexico
Russia
Peru
United Kingdom
Indonesia
Italy
Iran
Colombia
France
Argentina
Germany
Ukraine
South Africa
Spain
Poland
Turkey
Romania
Philippines
Chile
Hungary
Czechia
Ecuador
Malaysia
Canada
Bulgaria
Pakistan
Bangladesh
Belgium
Vietnam
Tunisia
Iraq
Thailand
Egypt
Netherlands
Bolivia
Burma
Greece
Portugal
Japan
Kazakhstan
Paraguay
Guatemala
Sweden
Slovakia
Morocco
Sri Lanka
Austria
Bosnia and Herzegovina
Georgia
Serbia
Jordan
Switzerland
Nepal
Croatia
Honduras
Moldova
Saudi Arabia
Lebanon
Cuba
Israel
Azerbaijan
Armenia
North Macedonia
Panama
Costa Rica
Afghanistan
Lithuania
Ethiopia
Uruguay
Algeria
Ireland
Libya
Slovenia
Kenya
Belarus
Venezuela
West Bank and Gaza
Zimbabwe
China
Latvia
Dominican Republic
South Korea
Oman
El Salvador
Zambia
Namibia
Uganda
Sudan
Albania
Denmark
Kosovo
Nigeria
Cambodia
Syria
Kyrgyzstan
Kuwait
Botswana
Jamaica
Montenegro
Trinidad and Tobago
Malawi
United Arab Emirates
Australia
Mongolia
Yemen
Mozambique
Senegal
Estonia
Cameroon
Angola
Uzbekistan
Finland
Bahrain
Rwanda
Somalia
Eswatini
Ghana
Suriname
Norway
Congo (Kinshasa)
Guyana
Madagascar
Luxembourg
Taiwan*
Mauritania
Singapore
Haiti
Tanzania
Cote d'Ivoire
Bahamas
Fiji
Lesotho
Mali
Qatar
Cyprus
Belize
Papua New Guinea
Malta
Guinea
Congo (Brazzaville)
Cabo Verde
Burkina Faso
Saint Lucia
Gabon
Maldives
Barbados
Togo
Mauritius
Laos
Nicaragua
Hong Kong
Djibouti
Equatorial Guinea
Benin
South Sudan
Andorra
Seychelles
Tajikistan
Timor-Leste
Central African Republic